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320 results • Page
2 of 7
Sort: Views
Rank
Views
Votes
Replies
1
vote
6
replies
418
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 15 days ago by
GenoMax
142k • written 4 weeks ago by
eebloom
▴ 80
1
vote
9
replies
412
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 9 days ago by
i.sudbery
19k • written 12 days ago by
Assa Yeroslaviz
★ 1.8k
0
votes
4
replies
407
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
6 days ago by
beginner123
• 0
2
votes
4
replies
387
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
25 days ago by
samuelkalandarov2002
▴ 10
1
vote
3
replies
384
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 20 days ago by
ATpoint
82k • written 21 days ago by
Francesco
▴ 10
0
votes
2
replies
371
views
How to update R on ubuntu
installation
update
R
apt-get
20 days ago by
Bosberg
▴ 50
0
votes
3
replies
368
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 19 days ago by
Ram
43k • written 5 months ago by
Fadi
• 0
1
vote
2
replies
363
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 5 days ago by
Ram
43k • written 6 days ago by
t.fortunato.asquini
• 0
0
votes
3
replies
355
views
Snakemake wrapper issue
fastqc
snakemake
updated 5 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
2
votes
3
replies
353
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 9 days ago by
bk11
★ 2.5k • written 14 days ago by
Yoosef
▴ 60
1
vote
4
replies
352
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 4 days ago by
Juke34
8.6k • written 6 days ago by
Vijith
▴ 30
3
votes
5
replies
350
views
Generating mpileup file using samtools
mpileup
samtools
updated 16 days ago by
Joe
21k • written 16 days ago by
Ruqaiya
• 0
1
vote
3
replies
343
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
13 days ago by
Lada
▴ 30
1
vote
3
replies
340
views
some error in building kraken2 database
metagenome
kraken2
25 days ago by
Art1ess
• 0
0
votes
0
replies
339
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
16 days ago by
NorbertK
▴ 10
2
votes
2
replies
339
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 24 days ago by
Ram
43k • written 25 days ago by
v.berriosfarias
▴ 140
5
votes
5
replies
334
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
11 days ago by
Chris
▴ 280
2
votes
3
replies
333
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 15 days ago by
dthorbur
★ 2.0k • written 16 days ago by
Vijith
▴ 30
1
vote
5
replies
332
views
Reconstruction of locus, order contigs
contigs
cluster
alignment
locus
updated 1 day ago by
dthorbur
★ 2.0k • written 2 days ago by
BATMAN
• 0
0
votes
1
reply
330
views
solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* error: could not open input file /geneInfo.tab #2142
STAR
updated 2 days ago by
GenoMax
142k • written 2 days ago by
huxiangyulove
• 0
0
votes
0
replies
331
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
25 days ago by
pramach1
▴ 40
1
vote
3
replies
330
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 18 days ago by
GenoMax
142k • written 18 days ago by
jeffrey.maurer.informatics
• 0
3
votes
4
replies
330
views
Truncated metadata file report from ENA Portal API
ena
python
8 days ago by
Giulia
• 0
0
votes
5
replies
326
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
6 days ago by
SilhouetteQ
• 0
0
votes
1
reply
326
views
Could you please assist in identifying this cluster?
single-cell
updated 29 days ago by
Ram
43k • written 4 weeks ago by
carolofharvest
▴ 40
1
vote
2
replies
325
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
18 days ago by
Nafi
• 0
0
votes
2
replies
324
views
bam merging for archaic samples
samtools
bam
updated 28 days ago by
Ram
43k • written 29 days ago by
Matteo Ungaro
▴ 100
0
votes
3
replies
324
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 19 days ago by
GenoMax
142k • written 19 days ago by
kim
• 0
0
votes
3
replies
324
views
KEGG Pathways
r
RNA-seq
updated 18 days ago by
Ram
43k • written 19 days ago by
Sudip
• 0
1
vote
4
replies
320
views
Help with Biopython for Beginner
Python
ORF
FASTA
Biopython
updated 1 day ago by
Joe
21k • written 10 days ago by
cput
• 0
0
votes
2
replies
315
views
Annovar using R package
Annovar
gnomAD
R
23 days ago by
DKA
▴ 40
0
votes
1
reply
314
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 12 days ago by
andres.firrincieli
3.6k • written 13 days ago by
Antonio
• 0
0
votes
6
replies
314
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
1 day ago by
hannes.bongartz
• 0
0
votes
4
replies
313
views
Correlation Analysis
statistics
methylation
NGS
expression
8 days ago by
Researcher
▴ 30
0
votes
2
replies
311
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 15 days ago by
yahn
• 0
0
votes
4
replies
310
views
Merge clusters in Seurat UMAP
seurat
umap
2 days ago by
kilcdincer
▴ 10
0
votes
4
replies
309
views
Genbank File Format
gbkformat
19 days ago by
alenew.am
• 0
1
vote
3
replies
309
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
26 days ago by
WouterDeCoster
47k
0
votes
1
reply
305
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 29 days ago by
GenoMax
142k • written 29 days ago by
bioyas
▴ 10
0
votes
2
replies
301
views
How are score_weights calculated in this code?
single-cell
8 days ago by
carolofharvest
▴ 40
0
votes
2
replies
299
views
Traveler with Infernal mapping failed
r2dt
updated 16 hours ago by
anton.i.petrov
• 0 • written 3 months ago by
Larissa
• 0
1
vote
3
replies
298
views
Odd alignment question/finding
Alignment
updated 16 days ago by
barslmn
★ 2.2k • written 17 days ago by
poordumbsillyidiot
• 0
1
vote
3
replies
294
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 8 days ago by
Ram
43k • written 9 days ago by
Omics data mining
▴ 260
1
vote
2
replies
294
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
17 days ago by
rianna.collins
• 0
3
votes
3
replies
291
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 5 days ago by
Ram
43k • written 19 days ago by
Adyasha
• 0
0
votes
2
replies
289
views
Downloading older version of a tool
Alignment
tools
15 days ago by
Ruqaiya
• 0
0
votes
5
replies
288
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 3 days ago by
GenoMax
142k • written 4 days ago by
chrisk
• 0
1
vote
2
replies
288
views
Downloading full alignments from Pfam
pfam
14 days ago by
bef1
• 0
0
votes
5
replies
286
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 11 days ago by
Joe
21k • written 11 days ago by
Lemonhope
• 0
0
votes
1
reply
286
views
creating batch colum for batch correction
batch-correction
combat
13 days ago by
Expert
▴ 10
320 results • Page
2 of 7
Recent Votes
plotting trees in R: node labels from nexus tree files
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
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Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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Comment: HGVS Nomenclature of Multiple Indels found in Cis
by
LauferVA
4.2k
how has this code progressed? is it publically available? would you want to work together?
Comment: Design for complex RNA-Seq experiment using Deseq2
by
Ezequiel
• 0
I completely agree with most points. The PCA shows that the biggest driver of difference is the patients themselves, with PRE and POST time…
Comment: Add stats to the plot
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marco.barr
▴ 130
Hi, you can add statistical annotations using `ggpubr` function `stat_pvalue_manual `. You need to make sure you calculate the p-values fir…
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
ATpoint
82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
Answer: CellRanger output more cells than specified using --force-cells? Why?
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▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data
by
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Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
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Fixed the issue by updating nucmer version.
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Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
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you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
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What is your question? It's unclear.
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One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
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See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
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Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
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